Aside

Jacob Arie

Contact Info

Skills

Languages

  • Fluent Dutch (Native language)
  • Fluent English (C2 level)
  • Basic swedish reading level (A2 reading level)

Programming languages

  • R
  • Python
  • Bash
  • SLURM

Main

Jacob Arie van Diermen

MSc, Research assistant

Education

Utrecht university, Graduate School of Life Sciences

MSc Molecular and Cellular life sciences (MCLS), specialization Biophysics & Molecular Imaging, Bioinformatics minor profile

Utrecht, The Netherlands

2023 - 2020

Final grade: 8.02/10

Bioinformatics minor profile

  • Thesis: Comparative genomics approach finds DNA-repair and immune-related genes in the regenerative African spiny mouse

Major research project

  • Thesis: Characterization of CSPP1 interaction with microtubules in cells

Utrecht university, Department of Biology

BSc in Biology

Utrecht, The Netherlands

2020 - 2017

graduated with honors (cum laude)

Final grade: 8.14/10

Bachelor thesis: Promising molecular targets for therapeutic intervention in Alzheimer’s disease

Research Experience

Research assistant

Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)

Solna, Sweden

Current - 2023/07


  • Continuation of the research project as a research assistant
  • Preparing and writing a manuscript for publication
  • Presenting data at lab meetings
  • Creating Docker and Singularity containers for the positive selection pipeline
  • Working with positive selection tools like HyPhy MEME. HyPhy aBSREL and PAML codeml
  • Experience working with the Linux operating system (Ubuntu, Pop!_OS)
  • Writing parallelized bash and R scripts for the positive selection pipeline
  • Accessing and working with publicly available single-cell datasets form GTEX

Teaching assistant

Utrecht university, Department of Biology

Utrecht, The Netherlands

2023/05 - 2023/02


Teaching assistant for the course Kwantitatieve biologie (B-B1KWBI20), a quantitative biology course for first year biology students. The course consists of a series of lectures and practicals in which students learn to use R for data analysis and statistics. As a teaching assistant, I supervised and the students during the practicals sessions.

Research intern

Karolinska Institutet, Clinical Neurosciences (Robert Harris Group)

Solna, Sweden

2023/03 - 2022/05


In my second year of my master ‘Molecular and Cellular life sciences’, I went to Stockholm for a 7 month internship position at Karolinska institute. This internship was part of my bioinformatics minor profile. At the Center for molecular medicine (CMM), and under the supervision of Sebastian Lewandowski, I performed a comparative genomics analysis which identified genes under positive selection in the regenerative African spiny mice (Acomys cahirinus), and attempting to link these genes to the regenerative phenotype. During this analysis, I build an independent analysis pipeline from scratch, using available software and functions in R, python and bash. This analysis pipeline was then executed on a large amount of genomics data, facilitated by a High performance computing (HPC) cluster. I see this internship as a big part in my development as a bioinformatician.

Skills aqcuired:

  • Bioinformatic analysis
  • Comparative genomics
  • Working with positive selection tools like HyPhy MEME and HyPhy aBSREL
  • Working with genomics data
  • Gene ontology analyses
  • Cytoscape and STRINGdb network analysis
  • Adept programming experience in R, Python and bash
  • Experience with High performance computing in a SLURM environment
  • Construction of a custom positive selection analysis pipeline for a large number of multiple sequence alignments
  • Experience with Git and github
  • Presenting and writing skills
  • Creation of a scientific poster for a conference
  • Creation of data visualizations using R

Research intern

Utrecht university, Cell biology, neurobiology and biophysics, Anna Akhmanova Group (Cellular dynamics)

Utrecht, The Netherlands

2022/03 - 2021/01


In my first year of the master ‘Molecular and Cellular life sciences’, I had an 9-month internship in Anna Akhmanova’s Lab which specializes in microtubule dynamics, under the supervision of Cyntha van den Berg. During these 9 months, I investigated the characteristics of CSPP1, a ciliary and centrosomal protein, and its effect on microtubule dynamics. Using immunofluorescence experiments and fluorescence microscopy, I tried to understand the effect of different domains of this protein on microtubule dynamics. For example, one domain of CSPP1 is important for microtubule binding, while another domain is crucial for microtubule stabilization. Furthermore, using Expansion microscopy I tried to investigate whether this protein is a microtubule inner protein (MIP), meaning that it binds to the inside of the microtubule. Finally, using live cell imaging and photoactivatable GFP, I examined the live-recruitment of this protein to the microtubules.

Skills acquired:

  • Extensive cell culture with mammalian adherent cell lines (COS7, RPE, HeLa)
  • Molecular cloning with SNAPtag, LEXY, PA-GFP, EB3 constructs
  • Transfections
  • Transformation of E.coli
  • Western blots (Semi-dry blotting)
  • PCR
  • Immunofluorescence staining
  • Fluorescence microscopy
  • Expansion microscopy (STED)
  • Live-cell imaging (spinning disk, TIRF)
  • Experiment planning
  • Presenting data
  • General lab skills

Additional skills

Programming languages

N/A

N/A


  • R (Experience in base R and a large number of R packages)
  • Python (Experience in base python and popular modules like numpy, pandas, matplotlib and machine learning modules like scikit-learn). Also experience with python single cell libraries like scanpy and anndata.
  • Bash (Experience in writing bash scripts for bioinformatics pipelines)
  • SLURM (Performing a large number of analyses using SLURM on HPC environments)

Software skills

N/A

N/A

  • STRING network analysis
  • gene ontology analysis
  • Cytoscape
  • Inkscape
  • Docker
  • Singularity
  • Git
  • Github
  • Rsudio
  • Anaconda
  • Visual studio code
  • Linux (Ubuntu, Pop!_OS)
  • HyPhy (aBSREL, MEME)
  • PAML codeml
  • Polyphen-2
  • MS word, Excel, PowerPoint
  • GraphPad Prism 8
  • Fiji/ ImageJ
  • Biorender
  • Reference managers (E.g. Mendeley, Zotero)

Talks and conferences

Genetic deconvolution of regenerative phenotypes in Acomys cahirinus

Tissue and Motion Conference 2022 (Poster)

Djurhamn, Sweden

2022

Aditya Singh, Sebastian A. Lewandowski, Katarina Tengvall, Michael Dong, Kerstin Lindblad-Toh

Recognition

Theme winner (Energy) Sustainable campus challenge 2020

Utrecht Challenge Alliance

Utrecht, The Netherlands

2020


I participated in the sustainable campus challenge 2020 organized by the Utrecht challenge alliance. This is a partnership for open innovation to find regional solutions to social issues in cooperation between companies, public organisations, governments and educational institutions. We were tasked to come up with a concept to reduce the energy usage of student housing and came up with a concept that rewards students for their sustainable behaviour. Our concept was chosen as the best concept to reduce student energy usage.

Latin honors (Cum laude) for BSc in Biology

Utrecht university, Department of Biology

Utrecht, The Netherlands

2020